error running OptKnock with TOMLAB_CPLEX

[Eugenio Gil]

Hi everyone,

So far I have used the gurobi solver succesfully to run optKnock and optGene on several models, but I'm having errors trying the same scripts with tomlab_cplex.

Currently, I'm trying the scripts provided with this paper. Files here.

The first error I came across with was the following:

Undefined function or variable 'updateStruct'.

Error in solveCobraMILP (line 439)
        tomlabProblem = updateStruct(tomlabProblem.MIP.cpxControl,solverParams);

Error in OptKnock (line 207)
    optKnockSol = solveCobraMILP(bilevelMILPproblem,'printLevel',verbFlag);

Error in Supplementary_Material_SM2 (line 196)
KnockSolution=OptKnock(model,selectedRxnList,options,constrOpt);

I tried looking for a file updateStruct in my cobratoolbox folder, and only found one called updateSructData, so I changed line 439 of solveCobraMILP, but then got a new error:

Reference to non-existent field 'probType'.

Error in tomRun (line 159)
   optType    = Prob.probType;

Error in solveCobraMILP (line 464)
        Result = tomRun('cplex', tomlabProblem);

Error in OptKnock (line 207)
    optKnockSol = solveCobraMILP(bilevelMILPproblem,'printLevel',verbFlag);

Error in Supplementary_Material_SM2 (line 196)
KnockSolution=OptKnock(model,selectedRxnList,options,constrOpt);

I'm surprised that I didn't experience any errors when using the Gurobi solver. Any pointers how to fix these issues with tomlab_cplex?

Thanks in advance,

[Ronan M.T. Fleming]

Hi,
that bug has been fixed previously
https://github.com/opencobra/cobratoolbox/issues/1449
are you using an older version of the cobra toolbox?
Regards,
Roann

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[Eugenio Gil]

Thank you Ronan,

Changing Line 439 to tomlabProblem.cpxControl = updateStructData(tomlabProblem.MIP.cpxControl,solverParams); as suggested in the link did solve my problems and now it seems to be running properly.





I believe my Cobra version is quite recent. I downloaded it not more than 2 months ago, and when running the log report it says "The COBRA Toolbox - 2020".

Best,

Eugenio Gil

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